The defense bill has cleared the Senate, and President Obama has withdrawn his veto threat, but concerns linger for some over whether a counterterrorism rider to the bill could deprive Americans of due process rights.

The US Senate on Thursday approved a controversial measure that affirms broad authority for the nation’s military to indefinitely detain suspected Al Qaeda members and associates captured in the United States.

The measure, a rider to the $662 billion Defense Authorization Act of 2012, was initially opposed by the Obama administration. It sparked sharp debate over whether the provision would allow detention without charge of US citizens seized on American soil.

Supporters downplayed the potential threat to civil liberties and offered compromise language to minimize the impact on US-based citizens. But critics denounced the measure as an ill-conceived expansion of executive and military power at the expense of due process rights.

Sen. John McCain (R) of Arizona, a co-sponsor, said in a floor speech that the measure was designed to address an inconsistency in Obama administration counterterrorism policy.

While Mr. Obama in September approved the killing of a US citizen in Yemen suspected of helping Al Qaeda, the administration has declined to authorize the open-ended military detention of Al Qaeda suspects captured in the US, Senator McCain said.

“You can kill them, capture them overseas, but when they get here we have to treat them as a common criminal,” he added.

McCain and Graham were referring to Anwar Al-Awlaki, the US-born Muslim cleric who was killed in a US drone missile attack Sept. 30.

Several senators contrasted the military option in Mr. Awlaki’s case with the handling of the so-called underwear bomber, who tried to blow up a jetliner over Detroit in Dec. 2009.

Nigerian citizen Umar Farouk Abdulmutallab was taken into the custody of the criminal justice system and given Miranda warnings that he had a right to a lawyer and a right to remain silent. Some senators suggested he should have been taken into military custody and subjected to aggressive interrogation without any warnings.

The counterterrorism rider requires the Obama administration to place in indefinite military custody Al Qaeda suspects involved in planning or carrying out an attack on US interests. It is designed to facilitate tough interrogations by military officials unconstrained by constitutional safeguards that apply to US law enforcement officials.

The bill exempts US citizens from the mandatory detention provision, but it does not exempt them from a broader authorization allowing the military to capture and hold anyone outside the US who is deemed to have supported Al Qaeda or associated forces.

The counterterrorism rider was softened during negotiations by adding a guarantee that it would not “affect existing law or authorities relating to the detention of United States citizens.”

Existing law on that subject is unclear. The US Supreme Court in 2004 upheld the indefinite detention of a US citizen captured on a foreign battlefield, but the high court has not ruled decisively on the legality of military detention without charge of a citizen captured within US borders or apprehended overseas beyond a battlefield.

Critics say military detention without trial violates fundamental principles of the US Constitution, including that the government must provide due process of law before depriving a citizen of liberty or property.

The new legislation is part of a long-running campaign by members of Congress to force the Obama administration to place a higher priority on the use of military options in the struggle against Al Qaeda and other suspected terrorists.

Administration officials had favored the use of the criminal justice system and federal courts over military detention and trials by military commission. But the administration’s apparent preference for civilian law enforcement – with full constitutional protections – prompted lawmakers to push back.

“What we are trying to do here is create policy that is as flexible as possible and that understands the difference between fighting a war and fighting crime,” Graham said during debate on the Senate floor last week. “We are fighting a war here.”

Obama threatened to veto the measure. But the White House withdrew that threat after lawmakers softened the provisions by allowing the executive branch to write its own regulations to implement military detentions, and by providing the president with broad discretion to waive the detention provision whenever he deems it is necessary to protect national security.

Among major provisions, the new law:

• Affirms broad authority for the military to indefinitely detain without trial any person believed by US government officials to have “substantially supported” Al Qaeda, the Taliban, or associated forces.

• Requires military detention for suspected foreign Al Qaeda operatives who government officials believe were involved in planning or carrying out an attack against the US.

• Requires the executive branch to establish procedures to conduct periodic status reviews of terror suspects held in open-ended military detention.

• Prohibits the use of funds to build or modify facilities in the US to house detainees transferred from the detention facilities at the US Naval Base, Guantanamo Bay, Cuba.

• Prohibits the use of funds to transfer Guantanamo detainees to the US for any reason, including for continued detention, trial in federal court, or release.

Civil rights and human rights advocates have criticized the bill as an embrace of police state tactics and as a retreat from the rule of law.

They complain that reliance on the military is unnecessary. In the past decade, more than 400 individuals have been prosecuted in US courts for terrorism-related offenses, while the military commission process had adjudicated six cases, critics say.

“The last time Congress passed indefinite detention legislation was during the McCarthy era and President Truman had the courage to veto that bill,” said Laura Murphy, director of the ACLU Washington legislative office, in a statement.

Kenneth Roth, executive director of Human Rights Watch, urged the White House to reverse its apparent decision to sign the counterterrorism rider into law. “By signing this defense spending bill, President Obama will go down in history as the president who enshrined indefinite detention without trial in US law,” he said.

Sen. Carl Levin (D) of Michigan, chairman of the Armed Services Committee and a co-sponsor of the bill, said it does not establish any broad, new powers.

“Those who say we have written into law a new authority are wrong,” he said.

Senator Levin said the ability to hold citizens without charge already exists under the law of war. An American citizen who joins a hostile force like Al Qaeda can be captured and detained indefinitely as an enemy combatant, he said.

Sen. Mark Udall (D) of Colorado said the difficulty with the military detention law is deciding who is enough of an enemy combatant to justify being locked up without charge potentially for the rest of his or her life.

“How do we go about determining who these individuals are,” Senator Udall asked. “The Constitution requires us to provide our citizens with due process before they are incarcerated, and especially before they are indefinitely incarcerated.”

Despite the compromise language in the rider, Graham insisted that there is “nothing that prevents us from holding one of our own for joining the enemy.”

He added: “I believe in due process. No one is going to prison without a federal judge’s oversight. No one stays in prison without a federal review.”